Image analysis from TEM and AFM micrograph, Table S1, S2, S3, Figure S1, Figure S2

We report on metal enrichment along a natural pH gradient owing to increased CO2 degassing at cold, shal- low seeps of Vulcano Island in the Mediterranean Sea, off Sicily. We assessed composition of unfiltered and filtered seawater (b100 nm) along acidic zones ranging between ambient and pH 5, and showed that most seep derived elements are present as nanoclusters which then aggregate into larger colloids while mixing with ambient seawater along a pH gradient. Size and elemental composition of such naturally occurring nanoparticles assessed by modern characterisation methods were in good agreement with the results from conventional analytical methods. We provide analytical evidence for the presence in the water column of a large fraction of seep derived ele- ments (e.g. approximately 50% of iron, over 80% of Mn, 100% of Cr, S and Zn) in the form of nano sized par- ticles (e.g. b100 nm) even at typical open ocean pHs. We launch in situ sampling protocols and sample preparation procedures for multi-method suitable to obtain accurate measurements on nanoparticles from environmental samples. Based on our results a first insight to the formation of natural nanoparticles at cold CO2 seeps is presented and the persistence of such nano-clusters in the surrounding seawater is stipulated.

Stable isotope (carbonates), organic carbon, calcium carbonate and occurrence of coccoliths at DSDP Hole 71-511

Thin but discrete pelagic limestone beds intercalated among the black mudstones near the top of the extensive Mesozoic black shale sequence of the Falkland Plateau are reminiscent of similar occurrences in the central and North Atlantic and may be cyclic in nature. They have been studied via carbonate, organic carbon, stable isotope, nannofloral, and ultrastructural analysis in an attempt to determine their mode of origin. Nannofossil diversity and preservation suggest that selective dissolution or diagenesis did not produce the interbedded coccolith-rich and coccolith-poor layers, nor did blooms of opportunistic species play a role. Stable isotope measurements of carbonate do not adequately constrain the origin of the cyclicity; however, the d13C data suggest that the more nannofossil-rich intervals may be due to higher nutrient supply and overturn of deeper waters at the site rather than influxes of well-oxygenated waters into an otherwise anoxic environment. Such an explanation is in accord with the nannofloral evidence

Petrography, minerals and isotopic composition at DSDP Leg 66 Holes

We collected 20 carbonate nodules from the inner trench slope deposits of the Middle America Trench area off Mexico. Carbonate nodules are found only within the methane-rich layer beneath the mixed layer of methane and hydrogen sulfide. They have been investigated by microscopic, scanning electron microscopic (SEM), X-ray diffraction, and stable isotopic analytical methods. Calcite, magnesian calcite, dolomite, and rhodochrosite were recognized as carbonate minerals. Each carbonate nodule is usually represented by single species of carbonate minerals. Carbonate nodules are subdivided into micrite nodules and recrystallized nodules according to textural features. The carbonate crystallites in each micrite nodule are equidimensional. Their sizes range from several to 30 µm, as revealed by SEM micrographs. The chemical composition of calcite is changed from pure calcite to high magnesian calcite, as shown by the shift of the (104) reflection in X-ray diffraction patterns. Fe substitution for Ca in dolomite was also observed. Carbon isotopic composition shows an unusually wide range - from -42.9 to +13.5 per mil - in PDB scale, whereas oxygen isotopic compositions of almost all the carbonate nodules are constantly enriched in 18O from +3.4 to +7.60 per mil in PDB scale. These wide variations in carbon isotopic composition indicate several sources for the carbon in carbonate nodules. Carbon with a negative d13C value was derived from biochemical oxidation of methane with a negative d13C value. On the other hand, carbon with positive d13C value was probably formed during methane production in an anoxic condition.

Miocene to Pleistocene diatom biostratigraphy with a focus on Thalassiosira in sediments of ODP Leg 186 sites

Late Neogene biostratigraphy of diatoms has been investigated from two sites occupied during Ocean Drilling Program (ODP) Leg 186 off the coast of northeast Japan. A unique aspect of ODP Leg 186 was the installation of two permanent borehole geophysical observatories at the deep-sea terrace along the Japan Trench. The Neogene subsidence history of the forearc was documented from both Sites 1150 and 1151, and Quaternary to middle Miocene (16 Ma) sediments represent a nearly continuous stratigraphic sequence including numerous ash records, especially during the past 9 m.y. Diatoms are found in most samples in variable abundance and in a moderately well preserved state throughout the sequence. The assemblages are characterized consistently by age-diagnostic species of Denticulopsis and Neodenticula found in regions of high surface water productivity typical of middle to high latitudes. The Neogene North Pacific diatom zonation divides the Miocene to Quaternary sequences fundamentally well, except that the latest Miocene through early Pliocene Thalassiosira oestrupii Subzone is not applicable. Miocene and late Pliocene through Pleistocene diatom datum levels that have been proven to be of great stratigraphic utility in the North Pacific Ocean appear to be nearly isochronous within the level of resolution constrained by core catcher sample spacing. The taxonomy and stratigraphy of previously described species determined to be useful across the Miocene/Pliocene boundary have been investigated on the basis of the evolutionary changes within the Thalassiosira trifulta group. The biostratigraphically important forms belonging to the genus Thalassiosira have been illustrated with scanning electron micrographs.

Culture experiments to evaluate CO2 effects on growth and morphology of the coccolithophore Pleurochrysis cf. pseudoroscoffensis

In the framework of the Italian project CO2 Monitor, two culture experiments were carried out in vertical closed photobioreactors with Pleurochrysis cf. pseudoroscoffensis Gayral & Fresnel 1983, a coccolithophore isolated from the Gulf of Trieste (North Adriatic Sea). The aim of this study was to investigate the effects induced by pH variations due to CO2 emissions on its growth and morphology. Two experiments were carried out with two different CO2 concentrations (1 and 2%). Growth and cell size in light microscopy, morphology and coccolith size in scanning electron microscopy, particulate nitrogen (PN) and particulate inorganic and organic carbon (PIC and POC) content of the coccolithophore were investigated during the light and dark phases. Dissolved inorganic nutrient (nitrate and phosphate) concentrations and pH of the medium and the presence of heterotrophic prokaryotes (HP) were monitored as well.

(Table 1) Gypsum, pyrite and glauconite at DSDP Hole 36-329

Authigenic gypsum, pyrite, and glauconite are disseminated throughout an unusually long (346 m) Miocene section of mixed biogenic carbonate and diatomaceous ooze drilled on the Falkland Plateau at DSDP Site 329 (water depth, 1519 m). The present organic carbon content of the sediment is low, ranging between 0.1 and 0.7%. Gypsum occurs as euhedral single or twinned crystals of selenite up to 5 mm in diameter, sometimes in the form of gypsum rosettes. These crystals are intact and unabraded, comprising up to 4% of the washed sample. The authigenic nature of the gypsum is demonstrated by the presence of diatoms and radiolarians embedded within the gypsum crystals. The gypsum co-occurs with pyrite and glauconite in these samples. The pyrite occurs as framboids, foraminiferal infillings, rods, and granular sheetlike masses composed of pyrite octahedra. The glauconite occurs as foraminiferal infillings and as free grains. The gypsum and pyrite were identified by energy-dispersive X-ray analysis and scanning electron micrographs. Some of the gypsum has grown on pyrite, indicating that it precipitated after the pyrite, perhaps in response to a change in pH conditions. The formation of the mineral suite can be explained by current models of in situ sulfide and sulfate precipitation coincident with diagenesis and oxidation of much of the original organic carbon.

Relative abundances of stratigraphically useful planktonic foraminifers from ODP Leg 167 sites

Late Neogene biostratigraphy of planktonic foraminifers has been investigated from 13 sites cored during Ocean Drilling Program Leg 167 off the coast of California. The planktonic foraminiferal biostratigraphy of six of these sites is presented here at higher stratigraphic resolution for the interval that encompasses the late early Pliocene through the Quaternary (~3.5 Ma to present day). The sites form a transect along the California margin from 31°N to 41°N within the California Current system. A new planktonic foraminiferal zonation has been established largely on evolutionary changes within the Neogloboquadrina plexus, supported by other taxa. A total of eight zones are recognized, most of which are broadly applicable throughout the region, thus providing a biostratigraphic zonation of the sequence at ~0.5-m.y. intervals. The new zonation appears to be unique to the California Current system. The diversity of planktonic foraminiferal assemblages during the late Neogene appears to have remained relatively constant despite large-scale paleoclimatic change. The assemblages are consistently dominated by few taxa that almost always include the neogloboquadrinids and Globigerina bulloides. Low diversity and high dominance of the assemblages favored these and other taxa well adapted to upwelling systems exhibiting high seasonal surface ocean variability. Apparently the oceanographic conditions that favor such assemblages have persisted at least for the duration of the late Neogene (~3.5 Ma to present day). The biostratigraphically important forms have been illustrated with scanning electron micrographs.

(Table 1) Statistics of size measurements of Lagenoeca antarctica sp. n. and Salpingoeca abyssalis sp. n. (floating form) sampled during POLARSTERN cruise ANT-XXII/2 and METEOR cruise M63/2

Despite their high abundance and their high importance for the oceanic matter flux, heterotrophic nanoflagellates are only poorly studied in the deep-sea regions. Studies on the choanoflagellate distribution during two deep-sea expeditions, to the South Atlantic (5038 m) and Antarctica (Weddell Sea, 2551 m), revealed the deepest records of choanoflagellates so far. A new species, (Lagenoeca antarctica) with a conspicuous spike structure on the theca is described from deep Antarctic waters. Lagenoeca antarctica sp. n. is a solitary unstalked free living salpingoecid-like choanoflagellate. The protoplast is surrounded by a typical theca with unique spikes only visible in SEM micrographs. The ovoid cell nearly fills the whole theca and ranges in size from 4 to 6 µm. The collar measures 2-3 µm and the flagellum 3-5 µm. A second species, Salpingoeca abyssalis sp. n., was isolated from the abyssal plain of the South Atlantic (5038 m depth). Floating and attached forms were observed. The protoplast ranges from to 2 to 4 µm in length and 1 to 2 µm in width. The collar is about the same length as the protoplast and the flagellum has 2 to 2.5 × the length of the protoplast. Phylogenetic analyses based on a fragment of SSU rDNA revealed Salpingoeca abyssalis to cluster together with a marine isolate of Salpingoeca infusionum while Lagenoeca antarctica clusters separately from the other codonosigid and salpingoecid taxa. Salpingoeca abyssalis and an undetermined Monosiga species seems to be the first choanoflagellate species recorded from the abyssal plain.

Benthic foraminifera in surface sediments of the Persian Gulf

During "Meteor"cruise 1965 the author collected 134 samples of surface sediments from the Iranian part of the Persian Gulf. Benthic Foraminifera populations have been analysed for determining their depth zonation. These data are supposed to allow detailed depth interpretation of Pleistocene sediments found in cores. In addition, the ecological information might be usefull to reconstruct the depositional environment of fossil sediments in similar shallow epicontinental seas. The investigation is published in two parts: the present part 1 contains the catalogue of species with short discussions of taxonomic problems, notes on the distribution within the Persian Gulf and 11 plates, partly with scanning electron micrographs. The results of the statistical analysis are given in data tables which include number of species, percentages of 2 (and 5) ranked species, standing crop and foraminiferal numbers. The author used "species groups" to avoid ambiguities with species requiring additional taxonomic studies. However, species numbers within these units are estimated to yield applicable diversity information. - A total of 52 species and 7 "species groups" were separated, 2 new species were described.

Sediment microstructures of ODP Leg 105 holes

Possible genetic relationships between syn- and post-depositional processes and sediment microstructure were investigated. Samples from cores at Sites 646 and 647 of Ocean Drilling Program (ODP) Leg 105 included examples of bottom current deposition (contourites), turbidity current deposition, consolidation, and diagenesis. Examination of nearly 200 micrographs of 14 samples from Site 646 and 13 samples from Site 647 leads to the conclusion that sedimentation processes do not appear to have an obvious influence on fabric. The effects of post-depositional processes, such as bioturbation, coring disturbance, and even remolding, appear to be less significant than one might expect as a result of the relatively coarse grain size of the sediments studied. Consolidation resulting from increased overburden stress results in increased particle alignment and compression of fabric elements with depth. The transition from open, random fabric in shallow samples to preferred orientation at depth represents the only change in these sediments that can be ascribed directly to a specific depositional or post-depositional process. Mineralogical variations, owing to changes in weathering processes and growth of authigenic/diagenetic minerals, also have a pronounced effect on sediment fabric.

Oxygen and carbon isotope ratios for six planktonic foraminifer species from different water depth, Ontong-Java Plateau, Pacific (Table 2)

Stable isotope analyses and scanning electron micrographs have been carried out on six planktonic forminifera species, Pulleniatina obliquiloculata, Globorotalia tumida, Sphaeroidinella dehiscens, Globigerinoides ruber, Globigerinoides sacculifer and Globigerinoides quadrilobatus from eleven box-cores taken at increasing depths in the equatorial Ontong-Java Plateau (Pacific). This allows us to describe the way dissolution affects the microstructures of the tests of the different species and to quantify the changes of isotopic composition. We may conclude that: 1) dissolution effects on test morphology and stable isotope compositions are species dependent, species with a similar habitat showing a similar trend; 2) the shallow water, thin-shelled species are the first to disappear: scanning electron microscope (SEM) work shows alteration of outer layers. Deep water, thick-shelled species are present in all samples: SEM work shows breakdown and disparition of inner layers; 3) for all species there is a similar trend towards increasing delta18O values with increasing water depths and increasing dissolution. This effect may be as high as 0.6 ? per thousand meters for Globorotalia tumida; 4) below the lysocline, around 3500 m, it appears that 13C/12C ratios slightly increase towards equilibrium values for thick shelled species: G. tumida, P. obliquiloculata and S. dehiscens. 14C dates and isotope stratigraphy of two box-cores show that all samples are recent in age, and exclude upward mixing of glacial deposits as an important factor.

Fragilariopsis kerguelensis images from sediment core PS1768-8

Background: Light microscopic analysis of diatom frustules is widely used both in basic and applied research, notably taxonomy, morphometrics, water quality monitoring and paleo-environmental studies. In these applications, usually large numbers of frustules need to be identified and / or measured. Although there is a need for automation in these applications, and image processing and analysis methods supporting these tasks have previously been developed, they did not become widespread in diatom analysis. While methodological reports for a wide variety of methods for image segmentation, diatom identification and feature extraction are available, no single implementation combining a subset of these into a readily applicable workflow accessible to diatomists exists. Results: The newly developed tool SHERPA offers a versatile image processing workflow focused on the identification and measurement of object outlines, handling all steps from image segmentation over object identification to feature extraction, and providing interactive functions for reviewing and revising results. Special attention was given to ease of use, applicability to a broad range of data and problems, and supporting high throughput analyses with minimal manual intervention. Conclusions: Tested with several diatom datasets from different sources and of various compositions, SHERPA proved its ability to successfully analyze large amounts of diatom micrographs depicting a broad range of species. SHERPA is unique in combining the following features: application of multiple segmentation methods and selection of the one giving the best result for each individual object; identification of shapes of interest based on outline matching against a template library; quality scoring and ranking of resulting outlines supporting quick quality checking; extraction of a wide range of outline shape descriptors widely used in diatom studies and elsewhere; minimizing the need for, but enabling manual quality control and corrections. Although primarily developed for analyzing images of diatom valves originating from automated microscopy, SHERPA can also be useful for other object detection, segmentation and outline-based identification problems.

The morphological response of Emiliania huxleyi to seawater carbonate chemistry changes: an inter-strain comparison

Four strains of the coccolithophore Emiliania huxleyi (RCC1212, RCC1216, RCC1238, RCC1256) were grown in dilute batch culture at four CO2 levels ranging from ~200 µatm to ~1200 µatm. Coccolith morphology was analyzed based on scanning electron micrographs. Three of the four strains did not exhibit a change in morphology over the CO2 range tested. One strain (RCC1256) displayed an increase in the percentage of malformed coccoliths with increasing CO2 concentration. We conclude that the sensitivity of the coccolith-shaping machinery to carbonate chemistry changes is strain-specific. Although it has been shown before that carbonate chemistry related changes in growth- and calcification rate are strain-specific, there seems to be no consistent correlation between coccolith morphology and growth or calcification rate. We did not observe an increase in the percentage of incomplete coccoliths in RCC1256, indicating that the coccolith-shaping machinery per se is affected by acidification and not the signalling pathway that produces the stop-signal for coccolith growth.

Magnetic and petrographic properties of ODP Site 120-747 (Table 1)

Carbonate sediments from the Kerguelen Plateau (ODP Leg 120) of Eocene to Pliocene age were investigated with rock magnetic, petrographic and geochemical methods to determine the carriers of remanent magnetization. Magnetic methods showed that the major magnetic minerals were titanomagnetites slightly larger than single domain particles. Submicrometre to micrometre-size grains of titanomagnetite were identified as inclusions in volcanic glass particles or as crystals in lithic clasts. Volcanic fallout ash particles formed the major fraction of the magnetic extract from each sediment sample. Three groups of volcanic ashes were identified: trachytic ashes, basaltic ashes with sideromelane and tachylite shards, and palagonitic ashes. These three groups could be equally well defined based on their magnetic hysteresis properties and alternating field demagnetization curves. The highest coercivities of all samples were found for the tachylite, due to the submicrometre-size titanomagnetite inclusions in the matrix. Trachytic ashes had intermediate magnetic properties between the single-domain-type tachylites and the palagonitic (altered) basaltic ashes with low coercivities. Samples which contained mixtures of these different volcanic ashes could be distinguished from the three types of ashes based on their magnetic characteristics. There was neither evidence of biogenic magnetofossils in the transmission electron micrographs nor did we find magnetic particles derived from continental Antarctica. The presence of dispersed volcanic fallout ashes between visible ash layers suggests continuous explosive volcanic activity on the Kerguelen Plateau in the South Indian Ocean since the early Eocene. The continuous fallout of volcanic ash from explosive volcanism on the Kerguelen Archipelago is the source of the magnetic particles and thus responsible for the magnetostratigraphy of the nannofossil oozes drilled during Leg 120.